A scientist named Tonio is reading a diary which belonged to a famous architect named Godey, his great-grandfather, indicating that two Pokémon between their dimension are fighting, and that the battle could lead to chaos. Those future events occur at same moment as Palkia, who can distort space, and Dialga, who rules over time, are brawling, which causes the hourglass in Tonio's lab to fall and shatter.